Contacts of the helix formed by residues 482 - 491 (chain B) in PDB entry 7CAL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 482 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377B LEU 5.8 0.8 + - - -
379B GLN 3.3 26.9 + - - -
380B GLY* 4.7 10.8 + - - -
381B VAL* 4.9 13.1 - - + +
480B HIS* 3.1 6.5 - - + -
481B ALA* 1.3 75.6 - - - +
483B ALA* 1.3 65.8 + - - +
484B ASP 3.2 2.2 - - - -
485B ASP* 3.0 28.1 + - + +
486B GLY* 3.1 17.0 + - - -
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Residues in contact with ALA 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B LEU* 3.8 35.2 - - + +
378B PHE* 4.5 17.5 - - + -
381B VAL* 5.9 2.2 - - + +
385B PHE* 5.2 2.9 - - + -
480B HIS* 4.0 19.4 + - + +
481B ALA 3.4 0.8 - - - -
482B HIS* 1.3 81.1 + - - +
484B ASP* 1.3 59.8 + - - +
486B GLY* 3.3 10.7 + - - +
487B ARG* 3.5 9.0 + - - +
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Residues in contact with ASP 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLY 3.7 20.9 - - - +
446B GLU* 4.9 11.3 - - - +
480B HIS 5.3 0.2 + - - -
481B ALA* 4.0 11.7 + - - +
482B HIS 3.2 0.6 - - - -
483B ALA* 1.3 77.6 - - - +
485B ASP* 1.3 58.2 + - - +
487B ARG* 4.1 9.3 + - - +
488B VAL* 4.2 10.9 + - - +
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Residues in contact with ASP 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B ALA 4.2 3.7 + - - +
482B HIS* 3.0 27.3 + - + +
484B ASP* 1.3 77.2 - - - +
486B GLY* 1.3 63.7 + - - +
487B ARG 3.2 3.1 + - - -
488B VAL* 3.4 26.0 + - - +
489B ILE* 3.6 15.5 - - - +
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Residues in contact with GLY 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B TYR* 3.9 24.4 - - - +
377B LEU* 4.7 6.5 - - - -
482B HIS* 3.1 20.1 + - - -
483B ALA* 3.3 6.1 + - - -
485B ASP* 1.3 76.5 - - - +
487B ARG* 1.3 60.6 + - - +
489B ILE* 3.9 14.3 + - - +
490B MET 3.9 6.4 + - - -
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Residues in contact with ARG 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B TYR* 4.5 7.0 + - + +
377B LEU* 3.8 23.1 - - + +
442B GLU* 5.5 7.6 - - + +
446B GLU* 3.3 20.9 - - - +
483B ALA 3.5 8.7 + - - +
484B ASP* 4.3 10.1 - - - +
485B ASP 3.2 0.6 - - - -
486B GLY* 1.3 77.0 - - - +
488B VAL* 1.3 64.1 + - - +
489B ILE 3.2 0.4 - - - -
490B MET* 3.3 13.0 + - - +
491B ASN* 3.3 16.8 + - - +
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B GLU* 4.3 14.5 + - - +
484B ASP 4.2 6.8 + - - +
485B ASP* 3.4 25.5 + - - +
487B ARG* 1.3 76.0 - - - +
489B ILE* 1.3 72.6 + - + +
491B ASN* 3.5 10.5 + - + -
492B ASN 3.3 23.6 + - - +
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Residues in contact with ILE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B ASP* 3.6 22.6 + - - +
486B GLY* 4.1 11.0 - - - +
487B ARG 3.2 0.6 - - - -
488B VAL* 1.3 82.5 - - + +
490B MET* 1.3 59.8 + - - +
492B ASN* 3.0 27.1 + - - +
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Residues in contact with MET 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B TYR* 3.5 56.3 - - + +
442B GLU* 4.6 7.4 - - - +
486B GLY 3.9 1.8 + - - -
487B ARG 3.3 6.7 + - - +
489B ILE* 1.3 79.8 - - - +
491B ASN* 1.3 73.0 + - - +
492B ASN* 3.2 12.9 + - - +
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Residues in contact with ASN 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B GLU* 3.0 29.0 - - - +
487B ARG* 3.3 14.6 + - - +
488B VAL* 3.5 10.7 + - + +
489B ILE 3.2 0.6 - - - -
490B MET* 1.3 93.0 + - - +
492B ASN* 1.3 70.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il